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Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development. The main disadvantage of existing methods is a lack of scalability. Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework. Our model accounts for incomplete lineage sorting through the coalescent model, and for horizontal inheritance of genes through reticulation nodes in the network. Computation of the pseudolikelihood is fast and simple, and it avoids the burdensome calculation of the full likelihood which can be intractable with many species. Moreover, estimation at the quartet-level has the added computational benefit that it is easily parallelizable. Simulation studies comparing our method to a full likelihood approach show that our pseudolikelihood approach is much faster without compromising accuracy. We applied our method to reconstruct the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), which is characterized by widespread hybridizations.

“El Aerolito” is the most biodiverse cenote cave globally, home to Poecilia velifera and Gambusia yucatana . However, their trophic niches and interactions remain undescribed. A total of 53 P. velifera and 38 G. yucatana were analyzed for stable isotopes, along with water samples for chlorophyll, silicates, and physical–chemical parameters. Data were collected during the norths, rainy, and dry seasons in the year 2023. Isotopic niches were calculated, and a PCA analysis was used to assess environmental factors. P. velifera showed δ[sup.13] C values of −25.4‰, −25.7‰, and −24.5‰, whereas G. yucatana exhibited −24.8‰, −24.0‰, and −24.2‰ across seasons. Niche size varied, with the largest during the norths and smallest during the rainy season, indicating seasonality. PCA linked environmental parameters (e.g., temperature and dissolved oxygen) to resource availability, suggesting niche shifts due to rainfall. Mangroves and insects contributed to the isotopic signals, with shifts observed during the dry and rainy seasons. The highest water parameter values occurred during the dry and rainy seasons, while the lowest was during the norths. The system, nutrient-poor and lacking chlorophyll production, relies on external sources. The study concludes that isotopic niches are dynamic and seasonally influenced by abiotic factors, especially rainfall.

Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H₂S)—a toxicant that impairs mitochondrial function—across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H₂S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H₂S in sulfide spring P. mexicana but not ancestral lineages from nonsulfidic habitats due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H₂S tolerance in different populations is likely caused by a combination of selection on standing genetic variation and de novo mutations. On a macroevolutionary scale, H₂S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes in genes associated with H₂S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and—in some instances—codons are implicated in H₂S adaptation in lineages that span 40 million years of evolution.

Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common—not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X . cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past approximately 40 generations of evolution. Finally, we compare our results to the well-studied X . birchmanni × X . malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X . birchmanni and X . cortezi .

This study tests the sensitivity of genetically based pest control options based on sex ratio distortion to intra- and intersexual aggressive interactions that affect male and female survival and fitness. Data on these interactions and their impacts were gathered for the mosquitofish Gambusia holbrooki (Poeciliidae), a promiscuous species with a strongly male-biased operational sex ratio and well-documented male harassment of females. The experimental design consisted of an orthogonal combination of two population densities and three sex ratios, ranging from strongly male-biased to strongly female-biased, and long-term observations of laboratory populations. Contrary to expectations, the number of males in a population had little evident effect on population demographics. Rather, the density of adult females determined population fecundity (as a result of a stock-recruitment relationship involving females, but not males), constrained male densities (apparently as a result of cannibalism or intersexual aggression), and regulated itself (most likely through effects of intrasexual aggression on female recruitment). The principal effect of males was to constrain their own densities via effects of male-male aggression on adult male mortality rates. Through use of a realistically parameterized genetic/demographic model, we show that of three different genetic options applied to control G. holbrooki, one based on recombinant sex ratio distortion (release of Female Lethal carriers) is marginally more efficient than a sterile male release program, and both outperform an option based on chromosomal sex ratio distortion (Trojan W). Nonlinear dependence of reproductive rate on female density reduces the efficacy of all three approaches. The major effect of intra- and intersexual aggression is mediated through females, whose interactions reduce female numbers and increase the efficacy of a control program based on sex ratio. Socially mediated male mortality has a small impact on control programs due to operational sex ratios that are heavily male-biased. The sensitivity of sex ratio-based control options to social factors will depend on the mating system of the targeted pest, but evidence of widespread density-dependent population regulation suggests that, for most species, the effects of elevated adult mortality (due to intra- and intersexual aggression) on control programs are likely to be slight.

In poeciliid fish, the evolution of the placenta is associated with polyandry in females and correlates with a suite of phenotypic and behavioural traits in males. Consequences of placenta evolution Females laying eggs for external fertilization have no control over the quality of the offspring, and must rely on proxies of male quality such as courtship and display traits. Evolutionary theory holds that all this changed with the advent of the placenta: with low-cost eggs incubated internally, a mother can hedge her bets, inspecting the genetic quality of her mates directly and provisioning her embryos accordingly. The resulting mother–offspring conflict is expected to lead to polyandry (females mating with multiple males) and to males that are smaller, less showy and more prone to opportunistic or 'sneaky' mating. Here Bart Pollux et al . test these ideas by looking at the Poecilidae — guppies and their relatives — a family of fish in which the various species show all varieties of internal and external fertilization, and in which the placenta has evolved at least eight times independently. This approach allows the authors to confirm that the evolution of the placenta is associated with polyandry in females, and smaller, less showy males that have longer penises to facilitate more opportunities for opportunistic mating. The evolution of the placenta from a non-placental ancestor causes a shift of maternal investment from pre- to post-fertilization, creating a venue for parent–offspring conflicts during pregnancy 1 , 2 , 3 , 4 . Theory predicts that the rise of these conflicts should drive a shift from a reliance on pre-copulatory female mate choice to polyandry in conjunction with post-zygotic mechanisms of sexual selection 2 . This hypothesis has not yet been empirically tested. Here we apply comparative methods to test a key prediction of this hypothesis, which is that the evolution of placentation is associated with reduced pre-copulatory female mate choice. We exploit a unique quality of the livebearing fish family Poeciliidae: placentas have repeatedly evolved or been lost, creating diversity among closely related lineages in the presence or absence of placentation 5 , 6 . We show that post-zygotic maternal provisioning by means of a placenta is associated with the absence of bright coloration, courtship behaviour and exaggerated ornamental display traits in males. Furthermore, we found that males of placental species have smaller bodies and longer genitalia, which facilitate sneak or coercive mating and, hence, circumvents female choice. Moreover, we demonstrate that post-zygotic maternal provisioning correlates with superfetation, a female reproductive adaptation that may result in polyandry through the formation of temporally overlapping, mixed-paternity litters. Our results suggest that the emergence of prenatal conflict during the evolution of the placenta correlates with a suite of phenotypic and behavioural male traits that is associated with a reduced reliance on pre-copulatory female mate choice.

The fish subfamily Poeciliinae (sensu Parenti, 1981) is widely distributed across the Western Hemisphere and a dominant component of the fish communities of Central America. Poeciliids have figured prominently in previous studies on the roles of dispersal and vicariance in shaping current geographic distributions. Most recently, Hrbek et al. combined a DNA-based phylogeny of the family with geological models to provide a biogeographic perspective that emphasized the role of both vicariance and dispersal. Here we expand on that effort with a database enlarged in the quantity of sequence represented per species, in the number of species included, and in an enlarged and more balanced representation of the order Cyprinodontiformes. We combine a robust timetree based upon multiple fossil calibrations with enhanced biogeographic analyses that include ancestral area reconstructions to provide a detailed biogeographic history of this clade. Key features of our results are that the family originated in South America, but its major diversification dates to a later colonization of Central America. We also resolve additional colonizations among South, Central and North America and the Caribbean and consider how this reconstruction contributes to our understanding of the mechanisms of dispersal.

The extent to which mate preferences are adaptive requires a better understanding of the factors that influence variation in mate preferences. Xiphophorus multilineatus is a live-bearing fish with males that exhibit alternative reproductive tactics (courter/sneaker). We examined the influence of a female’s genotype (courter vs sneaker lineage), growth rate, and social experience on mate preference for courter as compared to sneaker males. We found that females with a sneaker genotype and slower growth rates had stronger mate preferences for the faster growing courter males than females with a courter genotype, regardless of mating experience with one or both types of males. In addition, the relationship between strength of preference and growth rate depended on a females’ genotype; females with sneaker genotypes decreased their preference as their growth rates increased, a pattern that trended in the opposite direction for females from the courter genotypes. Disassortative mating preferences are predicted to evolve when heterozygous offspring benefit from increased fitness. Given male tactical dimorphism in growth rates and a mortality-growth rate tradeoff previously detected in this species, the variation in mating preferences for the male tactics we detected may be under selection to optimize the mortality-growth rate tradeoff for offspring.

Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments.